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Artificial intelligence (AI)-driven methods can vastly improve the historically costly drug design process, with various generative models already in widespread use. Generative models for de novo drug design, in particular, focus on the creation of novel biological compounds entirely from scratch, representing a promising future direction. Rapid development in the field, combined with the inherent complexity of the drug design process, creates a difficult landscape for new researchers to enter. In this survey, we organize de novo drug design into two overarching themes: small molecule and protein generation. Within each theme, we identify a variety of subtasks and applications, highlighting important datasets, benchmarks, and model architectures and comparing the performance of top models. We take a broad approach to AI-driven drug design, allowing for both micro-level comparisons of various methods within each subtask and macro-level observations across different fields. We discuss parallel challenges and approaches between the two applications and highlight future directions for AI-driven de novo drug design as a whole. An organized repository of all covered sources is available at https://github.com/gersteinlab/GenAI4Drug.

Dictionaries have been one of the central questions in data structures. A dictionary data structure maintains a set of key-value pairs under insertions and deletions such that given a query key, the data structure efficiently returns its value. The state-of-the-art dictionaries [Bender, Farach-Colton, Kuszmaul, Kuszmaul, Liu 2022] store $n$ key-value pairs with only $O(n \log^{(k)} n)$ bits of redundancy, and support all operations in $O(k)$ time, for $k \leq \log^* n$. It was recently shown to be optimal [Li, Liang, Yu, Zhou 2023b]. In this paper, we study the regime where the redundant bits is $R=o(n)$, and show that when $R$ is at least $n/\text{poly}\log n$, all operations can be supported in $O(\log^* n + \log (n/R))$ time, matching the lower bound in this regime [Li, Liang, Yu, Zhou 2023b]. We present two data structures based on which range $R$ is in. The data structure for $R

Augmented B-trees (aB-trees) are a broad class of data structures. The seminal work "succincter" by Patrascu showed that any aB-tree can be stored using only two bits of redundancy, while supporting queries to the tree in time proportional to its depth. It has been a versatile building block for constructing succinct data structures, including rank/select data structures, dictionaries, locally decodable arithmetic coding, storing balanced parenthesis, etc. In this paper, we show how to "dynamize" an aB-tree. Our main result is the design of dynamic aB-trees (daB-trees) with branching factor two using only three bits of redundancy (with the help of lookup tables that are of negligible size in applications), while supporting updates and queries in time polynomial in its depth. As an application, we present a dynamic rank/select data structure for $n$-bit arrays, also known as a dynamic fully indexable dictionary (FID). It supports updates and queries in $O(\log n/\log\log n)$ time, and when the array has $m$ ones, the data structure occupies \[ \log\binom{n}{m} + O(n/2^{\log^{0.199}n}) \] bits. Note that the update and query times are optimal even without space constraints due to a lower bound by Fredman and Saks. Prior to our work, no dynamic FID with near-optimal update and query times and redundancy $o(n/\log n)$ was known. We further show that a dynamic sequence supporting insertions, deletions and rank/select queries can be maintained in (optimal) $O(\log n/\log\log n)$ time and with $O(n \cdot \text{poly}\log\log n/\log^2 n)$ bits of redundancy., Comment: 33 pages, 1 figure; in FOCS 2023

A dictionary data structure maintains a set of at most $n$ keys from the universe $[U]$ under key insertions and deletions, such that given a query $x \in [U]$, it returns if $x$ is in the set. Some variants also store values associated to the keys such that given a query $x$, the value associated to $x$ is returned when $x$ is in the set. This fundamental data structure problem has been studied for six decades since the introduction of hash tables in 1953. A hash table occupies $O(n\log U)$ bits of space with constant time per operation in expectation. There has been a vast literature on improving its time and space usage. The state-of-the-art dictionary by Bender, Farach-Colton, Kuszmaul, Kuszmaul and Liu [BFCK+22] has space consumption close to the information-theoretic optimum, using a total of \[ \log\binom{U}{n}+O(n\log^{(k)} n) \] bits, while supporting all operations in $O(k)$ time, for any parameter $k \leq \log^* n$. The term $O(\log^{(k)} n) = O(\underbrace{\log\cdots\log}_k n)$ is referred to as the wasted bits per key. In this paper, we prove a matching cell-probe lower bound: For $U=n^{1+\Theta(1)}$, any dictionary with $O(\log^{(k)} n)$ wasted bits per key must have expected operational time $\Omega(k)$, in the cell-probe model with word-size $w=\Theta(\log U)$. Furthermore, if a dictionary stores values of $\Theta(\log U)$ bits, we show that regardless of the query time, it must have $\Omega(k)$ expected update time. It is worth noting that this is the first cell-probe lower bound on the trade-off between space and update time for general data structures., Comment: 38 pages; in FOCS 2023

In protein biophysics, the separation between the functionally important residues (forming the active site or binding surface) and those that create the overall structure (the fold) is a well-established and fundamental concept. Identifying and modifying those functional sites is critical for protein engineering but computationally non-trivial, and requires significant domain knowledge. To automate this process from a data-driven perspective, we propose a disentangled Wasserstein autoencoder with an auxiliary classifier, which isolates the function-related patterns from the rest with theoretical guarantees. This enables one-pass protein sequence editing and improves the understanding of the resulting sequences and editing actions involved. To demonstrate its effectiveness, we apply it to T-cell receptors (TCRs), a well-studied structure-function case. We show that our method can be used to alter the function of TCRs without changing the structural backbone, outperforming several competing methods in generation quality and efficiency, and requiring only 10% of the running time needed by baseline models. To our knowledge, this is the first approach that utilizes disentangled representations for TCR engineering.

Learning prerequisite chains is an essential task for efficiently acquiring knowledge in both known and unknown domains. For example, one may be an expert in the natural language processing (NLP) domain but want to determine the best order to learn new concepts in an unfamiliar Computer Vision domain (CV). Both domains share some common concepts, such as machine learning basics and deep learning models. In this paper, we propose unsupervised cross-domain concept prerequisite chain learning using an optimized variational graph autoencoder. Our model learns to transfer concept prerequisite relations from an information-rich domain (source domain) to an information-poor domain (target domain), substantially surpassing other baseline models. Also, we expand an existing dataset by introducing two new domains: CV and Bioinformatics (BIO). The annotated data and resources, as well as the code, will be made publicly available., Comment: Accepted by ACL 2021

Multi-label text classification (MLTC) is an attractive and challenging task in natural language processing (NLP). Compared with single-label text classification, MLTC has a wider range of applications in practice. In this paper, we propose a label-interpretable graph convolutional network model to solve the MLTC problem by modeling tokens and labels as nodes in a heterogeneous graph. In this way, we are able to take into account multiple relationships including token-level relationships. Besides, the model allows better interpretability for predicted labels as the token-label edges are exposed. We evaluate our method on four real-world datasets and it achieves competitive scores against selected baseline methods. Specifically, this model achieves a gain of 0.14 on the F1 score in the small label set MLTC, and 0.07 in the large label set scenario., Comment: 8 tables, 3 figures

This paper aims at providing the summary of the Global Data Science Project (GDSC) for COVID-19. as on May 31 2020. COVID-19 has largely impacted on our societies through both direct and indirect effects transmitted by the policy measures to counter the spread of viruses. We quantitatively analysed the multifaceted impacts of the COVID-19 pandemic on our societies including people's mobility, health, and social behaviour changes. People's mobility has changed significantly due to the implementation of travel restriction and quarantine measurements. Indeed, the physical distance has widened at international (cross-border), national and regional level. At international level, due to the travel restrictions, the number of international flights has plunged overall at around 88 percent during March. In particular, the number of flights connecting Europe dropped drastically in mid of March after the United States announced travel restrictions to Europe and the EU and participating countries agreed to close borders, at 84 percent decline compared to March 10th. Similarly, we examined the impacts of quarantine measures in the major city: Tokyo (Japan), New York City (the United States), and Barcelona (Spain). Within all three cities, we found the significant decline in traffic volume. We also identified the increased concern for mental health through the analysis of posts on social networking services such as Twitter and Instagram. Notably, in the beginning of April 2020, the number of post with #depression on Instagram doubled, which might reflect the rise in mental health awareness among Instagram users. Besides, we identified the changes in a wide range of people's social behaviors, as well as economic impacts through the analysis of Instagram data and primary survey data., Comment: 42 pages, 49 figures